Variant report

Variant	rs609760
Chromosome Location	chr8:69984351-69984352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:69764800..69767559-chr8:69983778..69986408,3	MCF-7	breast:
2	chr8:69754552..69756282-chr8:69983861..69986611,2	MCF-7	breast:
3	chr8:69765987..69767833-chr8:69983718..69985913,2	MCF-7	breast:
4	chr8:69937690..69940143-chr8:69983097..69986013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254337	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10957461	0.91[EUR][1000 genomes]
rs11774986	0.91[EUR][1000 genomes]
rs1344616	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1344617	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1344618	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs1344619	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1365412	0.96[ASN][1000 genomes]
rs1365413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1365414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1365416	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365418	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1465514	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1465515	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1541762	0.96[ASN][1000 genomes]
rs1559847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1559848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1965050	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1965698	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2042732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042734	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2042735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217103	0.96[ASN][1000 genomes]
rs28437123	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912509	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2912510	0.91[EUR][1000 genomes]
rs2912515	0.92[EUR][1000 genomes]
rs2912518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912520	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2981041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2981044	0.90[ASN][1000 genomes]
rs2981045	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981049	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981053	0.92[EUR][1000 genomes]
rs2981056	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981057	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981058	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981059	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981061	0.82[EUR][1000 genomes]
rs2981063	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2981065	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2981066	0.92[EUR][1000 genomes]
rs4358809	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs473477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs625096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62511793	1.00[ASN][1000 genomes]
rs639293	0.95[CHB][hapmap]
rs6472436	0.90[EUR][1000 genomes]
rs6472438	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031633	chr8:69766575-70322790	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv890987	chr8:69959105-70004698	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv1025578	chr8:69963284-69985807	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs609760	COPS5	cis	parietal	SCAN
rs609760	GUCY2E	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:69979600-69985200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr8:69980200-69984600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:69980600-69984800	Enhancers	HSMM	muscle
4	chr8:69981200-69985000	Enhancers	Osteobl	bone
5	chr8:69982200-69984400	Enhancers	NHLF	lung
6	chr8:69982400-69988200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr8:69982600-69984400	Enhancers	HSMMtube	muscle
8	chr8:69982800-69984400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:69982800-69984400	Enhancers	Hela-S3	cervix
10	chr8:69982800-69984400	Enhancers	HMEC	breast
11	chr8:69982800-69984600	Enhancers	NH-A	brain
12	chr8:69983000-69984400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:69983000-69984800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:69983200-69984400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:69983200-69984400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:69983400-69984400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:69983600-69984400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:69983800-69985000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr8:69984200-69984400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:69984200-69984400	Enhancers	NHEK	skin
21	chr8:69984200-69985200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:69984200-69985200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr8:69984200-69988200	Enhancers	NHDF-Ad	bronchial

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